| YjhC |
| ID: | 1517362693 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 372 (360) | ||
| Sequences: | 11646 (7450.9) | ||
| Seq/Len: | 32.350 | ||
| Nf(neff/√len): | 392.7 |
HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 32.350).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 53_D | 79_K | 3.923 | 1.00 |
| 101_V | 341_M | 3.444 | 1.00 |
| 81_A | 112_V | 3.309 | 1.00 |
| 74_K | 102_D | 3.192 | 1.00 |
| 130_R | 134_K | 3.091 | 1.00 |
| 3_N | 27_K | 3.008 | 1.00 |
| 128_Y | 131_K | 2.968 | 1.00 |
| 140_E | 245_T | 2.918 | 1.00 |
| 215_M | 350_A | 2.787 | 1.00 |
| 78_I | 106_A | 2.786 | 1.00 |
| 78_I | 102_D | 2.715 | 1.00 |
| 51_S | 54_A | 2.692 | 1.00 |
| 5_G | 55_L | 2.671 | 1.00 |
| 352_L | 356_Q | 2.639 | 1.00 |
| 74_K | 99_D | 2.629 | 1.00 |
| 82_K | 106_A | 2.614 | 1.00 |
| 108_K | 338_E | 2.584 | 1.00 |
| 121_N | 179_D | 2.547 | 1.00 |
| 78_I | 82_K | 2.476 | 1.00 |
| 68_T | 76_P | 2.442 | 1.00 |
| 86_H | 113_T | 2.331 | 1.00 |
| 72_L | 76_P | 2.310 | 1.00 |
| 131_K | 135_E | 2.294 | 1.00 |
| 75_E | 79_K | 2.287 | 1.00 |
| 74_K | 78_I | 2.233 | 1.00 |
| 4_Y | 63_C | 2.207 | 1.00 |
| 68_T | 72_L | 2.203 | 1.00 |
| 97_Y | 348_D | 2.201 | 1.00 |
| 64_V | 80_A | 2.164 | 1.00 |
| 101_V | 345_A | 2.148 | 1.00 |
| 128_Y | 132_L | 2.142 | 1.00 |
| 138_I | 244_G | 2.119 | 1.00 |
| 105_K | 109_E | 2.117 | 1.00 |
| 132_L | 137_V | 2.098 | 1.00 |
| 106_A | 110_A | 2.077 | 1.00 |
| 96_S | 99_D | 2.072 | 1.00 |
| 77_V | 89_C | 2.062 | 1.00 |
| 77_V | 103_M | 2.038 | 1.00 |
| 101_V | 105_K | 2.036 | 1.00 |
| 61_V | 85_K | 2.019 | 1.00 |
| 141_I | 242_I | 1.976 | 1.00 |
| 38_E | 42_R | 1.966 | 1.00 |
| 190_E | 218_E | 1.943 | 1.00 |
| 117_G | 314_E | 1.923 | 1.00 |
| 129_A | 249_I | 1.923 | 1.00 |
| 82_K | 109_E | 1.923 | 1.00 |
| 114_F | 337_G | 1.892 | 1.00 |
| 52_L | 79_K | 1.877 | 1.00 |
| 81_A | 107_C | 1.872 | 1.00 |
| 219_F | 225_A | 1.868 | 1.00 |
| 5_G | 61_V | 1.865 | 1.00 |
| 30_C | 49_M | 1.847 | 1.00 |
| 178_L | 346_T | 1.831 | 1.00 |
| 187_E | 221_S | 1.829 | 1.00 |
| 14_A | 43_E | 1.797 | 1.00 |
| 342_S | 345_A | 1.795 | 1.00 |
| 130_R | 183_H | 1.782 | 1.00 |
| 104_V | 337_G | 1.781 | 1.00 |
| 50_S | 54_A | 1.768 | 1.00 |
| 190_E | 220_P | 1.760 | 1.00 |
| 86_H | 112_V | 1.729 | 1.00 |
| 95_L | 99_D | 1.697 | 1.00 |
| 74_K | 103_M | 1.684 | 1.00 |
| 66_V | 77_V | 1.673 | 1.00 |
| 349_A | 353_S | 1.667 | 1.00 |
| 3_N | 62_D | 1.665 | 1.00 |
| 317_F | 321_I | 1.652 | 1.00 |
| 187_E | 220_P | 1.650 | 1.00 |
| 82_K | 110_A | 1.643 | 1.00 |
| 142_L | 245_T | 1.639 | 1.00 |
| 104_V | 341_M | 1.636 | 1.00 |
| 320_N | 324_G | 1.601 | 1.00 |
| 100_C | 341_M | 1.576 | 1.00 |
| 189_P | 220_P | 1.573 | 1.00 |
| 63_C | 318_L | 1.563 | 1.00 |
| 182_Q | 188_I | 1.563 | 1.00 |
| 79_K | 82_K | 1.535 | 1.00 |
| 3_N | 29_T | 1.533 | 1.00 |
| 94_A | 99_D | 1.522 | 1.00 |
| 52_L | 76_P | 1.517 | 1.00 |
| 336_N | 339_A | 1.511 | 1.00 |
| 1_M | 27_K | 1.509 | 1.00 |
| 145_H | 241_I | 1.499 | 1.00 |
| 191_T | 218_E | 1.494 | 1.00 |
| 138_I | 247_G | 1.490 | 1.00 |
| 100_C | 344_I | 1.486 | 1.00 |
| 97_Y | 101_V | 1.484 | 1.00 |
| 9_V | 31_V | 1.480 | 1.00 |
| 37_G | 41_A | 1.479 | 1.00 |
| 49_M | 55_L | 1.472 | 1.00 |
| 30_C | 55_L | 1.470 | 1.00 |
| 52_L | 56_V | 1.459 | 1.00 |
| 182_Q | 219_F | 1.447 | 1.00 |
| 349_A | 360_V | 1.442 | 1.00 |
| 79_K | 83_N | 1.421 | 1.00 |
| 23_H | 316_L | 1.416 | 1.00 |
| 57_S | 83_N | 1.401 | 0.99 |
| 78_I | 103_M | 1.391 | 0.99 |
| 69_P | 72_L | 1.390 | 0.99 |
| 55_L | 61_V | 1.373 | 0.99 |
| 2_I | 63_C | 1.372 | 0.99 |
| 56_V | 80_A | 1.370 | 0.99 |
| 190_E | 361_K | 1.360 | 0.99 |
| 182_Q | 342_S | 1.351 | 0.99 |
| 138_I | 141_I | 1.350 | 0.99 |
| 99_D | 102_D | 1.346 | 0.99 |
| 192_V | 359_K | 1.336 | 0.99 |
| 185_L | 223_K | 1.334 | 0.99 |
| 352_L | 355_S | 1.319 | 0.99 |
| 39_N | 43_E | 1.316 | 0.99 |
| 103_M | 114_F | 1.309 | 0.99 |
| 181_V | 225_A | 1.304 | 0.99 |
| 94_A | 103_M | 1.303 | 0.99 |
| 106_A | 109_E | 1.293 | 0.99 |
| 182_Q | 339_A | 1.292 | 0.99 |
| 66_V | 76_P | 1.292 | 0.99 |
| 20_M | 65_I | 1.291 | 0.99 |
| 59_K | 85_K | 1.285 | 0.99 |
| 319_H | 323_C | 1.281 | 0.99 |
| 348_D | 352_L | 1.278 | 0.99 |
| 138_I | 249_I | 1.273 | 0.99 |
| 97_Y | 345_A | 1.268 | 0.99 |
| 356_Q | 360_V | 1.263 | 0.99 |
| 131_K | 134_K | 1.262 | 0.99 |
| 132_L | 135_E | 1.260 | 0.99 |
| 5_G | 32_Y | 1.257 | 0.99 |
| 81_A | 87_V | 1.254 | 0.99 |
| 4_Y | 26_A | 1.248 | 0.99 |
| 25_N | 323_C | 1.246 | 0.98 |
| 105_K | 108_K | 1.244 | 0.98 |
| 121_N | 339_A | 1.243 | 0.98 |
| 37_G | 48_N | 1.242 | 0.98 |
| 93_I | 100_C | 1.239 | 0.98 |
| 178_L | 347_A | 1.234 | 0.98 |
| 32_Y | 52_L | 1.233 | 0.98 |
| 80_A | 87_V | 1.230 | 0.98 |
| 81_A | 106_A | 1.226 | 0.98 |
| 49_M | 58_S | 1.226 | 0.98 |
| 94_A | 100_C | 1.220 | 0.98 |
| 241_I | 250_K | 1.196 | 0.98 |
| 36_N | 39_N | 1.187 | 0.98 |
| 133_I | 184_L | 1.181 | 0.98 |
| 144_C | 242_I | 1.170 | 0.97 |
| 89_C | 116_A | 1.154 | 0.97 |
| 32_Y | 55_L | 1.154 | 0.97 |
| 54_A | 58_S | 1.152 | 0.97 |
| 53_D | 57_S | 1.150 | 0.97 |
| 144_C | 181_V | 1.150 | 0.97 |
| 54_A | 57_S | 1.148 | 0.97 |
| 81_A | 110_A | 1.143 | 0.97 |
| 104_V | 108_K | 1.139 | 0.97 |
| 30_C | 61_V | 1.138 | 0.97 |
| 89_C | 114_F | 1.135 | 0.97 |
| 98_E | 102_D | 1.134 | 0.97 |
| 141_I | 185_L | 1.133 | 0.97 |
| 352_L | 360_V | 1.125 | 0.97 |
| 144_C | 185_L | 1.124 | 0.97 |
| 97_Y | 341_M | 1.115 | 0.96 |
| 102_D | 105_K | 1.111 | 0.96 |
| 76_P | 79_K | 1.109 | 0.96 |
| 60_L | 85_K | 1.107 | 0.96 |
| 145_H | 228_E | 1.106 | 0.96 |
| 312_R | 316_L | 1.105 | 0.96 |
| 349_A | 362_I | 1.104 | 0.96 |
| 84_K | 110_A | 1.101 | 0.96 |
| 181_V | 219_F | 1.098 | 0.96 |
| 93_I | 116_A | 1.090 | 0.96 |
| 34_P | 38_E | 1.081 | 0.95 |
| 127_Q | 131_K | 1.077 | 0.95 |
| 58_S | 61_V | 1.077 | 0.95 |
| 144_C | 225_A | 1.075 | 0.95 |
| 188_I | 220_P | 1.074 | 0.95 |
| 47_I | 58_S | 1.064 | 0.95 |
| 318_L | 322_L | 1.059 | 0.95 |
| 102_D | 106_A | 1.057 | 0.95 |
| 113_T | 325_A | 1.055 | 0.95 |
| 141_I | 244_G | 1.052 | 0.95 |
| 58_S | 85_K | 1.050 | 0.94 |
| 349_A | 352_L | 1.040 | 0.94 |
| 313_K | 316_L | 1.038 | 0.94 |
| 77_V | 87_V | 1.037 | 0.94 |
| 3_N | 61_V | 1.026 | 0.94 |
| 39_N | 42_R | 1.018 | 0.93 |
| 107_C | 337_G | 1.017 | 0.93 |
| 113_T | 324_G | 1.015 | 0.93 |
| 107_C | 114_F | 1.012 | 0.93 |
| 129_A | 251_I | 1.008 | 0.93 |
| 188_I | 342_S | 1.001 | 0.92 |
| 320_N | 326_K | 1.000 | 0.92 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 1h6dA | 12 | 0.9086 | 100 | 0.254 | Contact Map |
| 1zh8A | 2 | 0.8441 | 100 | 0.262 | Contact Map |
| 3dtyA | 4 | 0.9247 | 100 | 0.265 | Contact Map |
| 2nvwA | 2 | 0.8952 | 100 | 0.267 | Contact Map |
| 3v5nA | 4 | 0.879 | 100 | 0.27 | Contact Map |
| 3euwA | 4 | 0.8817 | 100 | 0.28 | Contact Map |
| 3e18A | 2 | 0.9462 | 100 | 0.283 | Contact Map |
| 3ceaA | 4 | 0.8844 | 100 | 0.283 | Contact Map |
| 3q2iA | 1 | 0.879 | 100 | 0.283 | Contact Map |
| 3oqbA | 8 | 0.922 | 100 | 0.283 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)